A Comparative Structure–Function Analysis and Molecular Mechanism of Action of Endonucleases from Serratia marcescens and Physarum polycephalum

Structural and functional characteristics were compared for wild-type nuclease from Serratia marcescens, which belongs to the family of DNA/RNA nonspecific endonucleases, its mutational forms, and the nuclease I-PpoI from Physarum polycephalum, which is a representative of the Cys-His box-containing subgroup of the superfamily of extremely specific intron-encoded homing DNases. Despite the lack of sequence homology and the overall different topology of the Serratia marcescens and I-PpoI nucleases, their active sites have a remarkable structural similarity. Both of them have a unique magnesium atom in the active site, which is a part of the coordinatively bonded water–magnesium complex involved in their catalytic acts. In the enzyme–substrate complexes, the Mg²⁺ ion is chelated by an Asp residue, coordinates two oxygen atoms of DNA, and stabilizes the transition state of the phosphate anion and 3"-OH group of the leaving nucleotide. A new mechanism of the phosphodiester bond cleavage, which is common for the Serratia marcescens and I-PpoI nucleases and differs from the known functioning mechanism of the restriction and homing endonucleases, was proposed. It presumes a His residue as a general base for the activation of a non-cluster water molecule at the nucleophilic in line displacement of the 3"-leaving group. A strained metalloenzyme–substrate complex is formed during hydrolysis and relaxes to the initial state after the reaction.     

Nutritional estimate of populations of some wild free-ranging African ungulates in grassland (Nechisar national park, Ethiopia) in dry season

The amount and nutritive value of forage plants, diet composition, digestibility of dry matter and nutrients were recorded for zebra. Grant's gazelle, Swayne's hartebeest and hippopotamus in November-December 1991 Besides, daily egest of feces, the level of food and nutrient consumption, energy and protein requirements were recorded for zebra and Grant's gazelle The digestibility of pasture forage was determined as a ratio of lignin concentration in food to the concentration m feces (lignin tracer technique), a daily intake was calculated on the basis of the daily feces egest Protein percentage m the diet of zebra and hartebeest consuming dry parts of grasses did not exceed 5% Gazelle diet consists of green parts of plants and included 18% of protein The digestibility of dry matter in nonruminants (zebra, hippopotamus) was 40-45%, in hartebeest - 50%, in gazelle - 60% Due to the abundance of dry grasses (3 7 ton ha^-1) the daily food consumption of zebra was high - 7 2 kg ind^-1 (dry weight), the metabolizable energy intake (ME) being 51 MJ Adult gazelles consumed 15-25 kg ind^-1 of food and 14-24 MJ of ME The energy requirements of adult males and non-lactating females of zebras and gazelles (48 and 13 MJ respectively) were met, the energy balance berig negative for lactating animals The daily protein requirement was not met in zebra (392-704 g md^-1 vs 134 g ind^-1 of intake) and in lactating gazelles (250 g ind^-1 vs 197 g md^-1) Non-lactating gazelles consume sufficient amount of both energy and protein due to the high feeding selectivity of the species and thanks to the abundance of burnt areas with young green after-grass m the dry period     

Multiparticle computer simulation of photosynthetic electron transport in a thylakoid membrane

A method for multiparticle computer simulation of photosynthetic electron transport in a thylakoid membrane has been developed. The basic principles of this method were described previously. The method is used to describe the cyclic electron flow around photosystem I. The effects of size and shape of the reaction volume on the kinetics of interaction of a mobile carrier with a protein complex and the limited diffusion of reactants were studied. It was shown that the kinetic parameters of photosynthetic electron transport processes depend on the distribution of protein complexes in the membrane. It was shown that the limited nature of diffusion of plastoquinone molecules in the membrane leads to a tenfold decrease in the efficient diffusion coefficient. It was shown that the occurrence of two phases of dark reduction of photooxidized P700+ is due to a heterogeneous spatial organization of the thylakoid membrane of a chloroplast.     

Fodder resources and feeding of semifree bison (<Emphasis Type="Italic">Bison bison</Emphasis>) on a steppe pasture in the Western Manych valley

In 2012–2013, the species composition, aboveground phytomass, and nutrition of freely ranging bison were investigated on a natural steppe pasture of the Western Manych valley. The aboveground mass of plants on the investigated pasture varied from 16.1 to 19.4 c/ha. The composition of the plants consumed by bison and their share in the bison’s diet were determined by microscopy of feces. In the snowless season, graminoids was the basis of the bison’s diet (79–87%). The use of forbs varied from 4.7 to 17.5%. Sedges were present in the forage in summer; they amounted to 6.5–15.4%. The quantitative assessment of the food selectivity was determined using the ratio of the share of a plant species in the diet to its portion in the plant community of the pasture. The most selected were Festuca valesiaca (the selectivity is 12.0), Agropyron sp. sp. (1.7), Polygonum patulum (1.2), and Carex sp. sp. (1.1). In other forage plants (Poa bulbojsa, Tanacetum achileifolium, and other forbs), the selectivity was 0.01–0.3. The nutritional value of fodder vegetation and food indexes (daily intake, digestibility of forage, consumption of metabolizable energy) were estimated. The digestibility was determined by the ratio of inert (undigestible) components (silicon, lignin) in the diet to their amount in the feces. The daily intake of forage was calculated based on the mass of released feces and digestibility of forage. In the snowless season, bison consumed from 6.3–7.0 to 9.2–9.9 kg/ind. (dry weight) per day. The maximum consumption (9.9 kg/ind.) was observed in summer. The digestibility of forage changed from 45 to 53% (the average is 50%). The consumption of metabolizable energy in different seasons varied from 0.60 to 0.91 MJ/kg^0.75/day, which corresponded to maintenance energy.     

Crystallographic and NMR spectroscopic protein structures: the inter-residue contacts

Inter-residue pair contacts have been analyzed in detail for the four pairs of protein structures determined both by X-ray analysis (X-ray) and nuclear magnetic resonance (NMR). At contact distances < or = 4.0 angstroms in the four NMR structures the overall number of pair contacts are less by 4-9% and pair contacts are in average shorter by 0.02-0.16 angstroms than those in corresponding X-ray structures. In each of four structure pairs 83-94% of common pair contacts are formed by the same residues in both structures and rest 6-17% ones are longer own pair contacts formed by the different residues in the NMR and X-ray structures. The amount of the longer own contacts is higher in the X-ray structure of the pair. In the each NMR structure there are three types of common pair contacts, which are shorter, longer or equal length in comparison with identical pair contacts in the X-ray structure of the same protein. The methodological different shortened common pair contacts predominate in the known distant dependence of the inter-residue contact densities of the 60-61 pair of the NMR/X-ray structure. Among four pairs analyzed the contact shortening proceeds upon the energy minimization of the crambin NMR structure and upon the resolving by the program X-PLOR with decreased atom van der Waals radius of the NMR structures of ubiquitin, hen lysozyme and monomeric hemoglobin. An extent of the NMR contact shortening decreased as the amount of NMR information upon the calculation of the NMR structures increased. Among 60-61 pairs of NMR/X-ray structures the main difference between alpha-helical and beta-structural proteins on the inter-residue distant dependence of the average contact densities arises from the strong alpha/beta difference in the local backbone geometry.